Align 3-hydroxypropionate dehydrogenase (EC 1.1.1.59) (characterized)
to candidate AO356_30225 AO356_30225 choline dehydrogenase
Query= metacyc::MONOMER-15202 (579 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_30225 Length = 546 Score = 356 bits (914), Expect = e-102 Identities = 216/546 (39%), Positives = 312/546 (57%), Gaps = 27/546 (4%) Query: 36 FDYIVVGAGTAGCLLANRLSADPANRVLLIEAGGRDNYHWIHIPVGYLYCINNPRTDWRF 95 +DYIVVGAG++GC +A LS DP N VLLIEAG + W++ P G N +W F Sbjct: 4 YDYIVVGAGSSGCPVARGLSDDPRNNVLLIEAGPASDRFWVNTPAGMGKLYFNKSLNWNF 63 Query: 96 RTEPDPGLNGRSLIYPRGKTLGGCSSINGMLYLRGQARDYDGWAELTGDDAWRWDNCLPD 155 RT P L GR + +PRGK LGG SSINGM+++RG +D+DGW L G+ W +++ LP Sbjct: 64 RTSPMEKLQGRRMYWPRGKLLGGSSSINGMVFIRGHQKDFDGWRAL-GNPGWGYEDVLPY 122 Query: 156 FMRHEDHYRLDEGGDADPDHYKFHGHGGEWRIEKQRLKWQVLADFATAAVEAGVPRTRDF 215 F + E + GGD ++ G G I +K + DF AA G+P T D Sbjct: 123 FKKME---HFERGGD------EYRGANGPLWISDPVVKEKSSYDFIEAANRIGIPVTEDM 173 Query: 216 NRGDNEGVDAFEVNQRSGWRWNASKAFLRGVEQRGNLTVWHSTQVLKLDFASGEGSEPRC 275 N ++GV + N + G R + +AF+ V +R NLTV ++ ++ F EG Sbjct: 174 NGALHDGVGFMQHNIQDGQRMSTYRAFIEPVIERPNLTVRTGCELQRVLF---EGR--TA 228 Query: 276 CGVTVERAGKKVVTTARCEVVLSAGAIGSPQLLQLSGIGPTALLAEHAIPVVADLPGVGE 335 G+ V ++G+ A EV+LSAG++ +PQ+L LSGIGP A L +HAIP V + PGVG+ Sbjct: 229 VGIEVLKSGRLERIYAAREVILSAGSLKTPQMLMLSGIGPRAELEKHAIPEVLNSPGVGQ 288 Query: 336 NLQDHLQIRSIYKVKGAKTLNTMANSLIGKAKI--GLEYILKRSGPMSMAPSQLCIFTRS 393 NLQDH I + ++ + N +L+G K G Y++ R G +++ SQ+ F +S Sbjct: 289 NLQDHFYIHTAFRCTPDSSYNA---NLVGLRKYWEGFRYLMTRKGYLALGSSQVAAFVKS 345 Query: 394 SKEYEHPNLEYHVQPLSLEAFGQPLHD---FPAITASVCNLNPTSRGTVRIKSGNPRQAP 450 S + ++ +L+ +P++ + F D P + SV L P++ GTV ++S NP Sbjct: 346 SPDEDYADLQISFRPMTFQYFPDGTVDVERHPGLGVSVYQLRPSTTGTVTLRSTNPSDPA 405 Query: 451 AISPNYLSTEEDRQVAADSLRVTRHIA-SQPAFAKYDPEEFKPGVQYQSDEDLARLAGDI 509 +PN+LS++ D +R R I S+P ++ EE PG+ ++DED+ + Sbjct: 406 DYTPNFLSSDYDVNAVISGVRWIRKIMNSEPIKSRVVSEEL-PGLHIRTDEDIYNYLVET 464 Query: 510 GTTIFHPVGTAKMGRDDDPMAVVDSHLRVRGVTGLRVVDASIMPTITSGNTNSPTLMIAE 569 G + H GT KMG +D MAVVD LRVRG+ LRVVDASIMP ITSGNTN+P++MI Sbjct: 465 GNSAHHQGGTCKMG--NDAMAVVDERLRVRGIERLRVVDASIMPFITSGNTNAPSIMIGV 522 Query: 570 KAAGWI 575 KAA I Sbjct: 523 KAADLI 528 Lambda K H 0.318 0.135 0.418 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 882 Number of extensions: 39 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 579 Length of database: 546 Length adjustment: 36 Effective length of query: 543 Effective length of database: 510 Effective search space: 276930 Effective search space used: 276930 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory